A structural basis for processivity

Protein Science - Tập 10 Số 9 - Trang 1699-1711 - 2001
Wendy A. Breyer1, Brian W. Matthews2,1
1Institute of Molecular Biology, Howard Hughes Medical Institute, and Department of Physics, University of Oregon, Eugene, Oregon 97403‐1229, USA
2Dr. Brian W. Matthews, Institute of Molecular Biology, 1229 University of Oregon, Eugene, OR 97403‐1229, USA.

Tóm tắt

AbstractThe structures of a number of processive enzymes have been determined recently. These proteins remain attached to their polymeric substrates and may perform thousands of rounds of catalysis before dissociating. Based on the degree of enclosure of the substrate, the structures fall into two broad categories. In one group, the substrate is partially enclosed, while in the other class, enclosure is complete. In the latter case, enclosure is achieved by way of an asymmetric structure for some enzymes while others use a symmetrical toroid. In those cases where the protein completely encloses its polymeric substrate, the two are topologically linked and an immediate explanation for processivity is provided. In cases where there is only partial enclosure, the structural basis for processivity is less obvious. There are, for example, pairs of proteins that have quite similar structures but differ substantially in their processivity. It does appear, however, that the enzymes that are processive tend to be those that more completely enclose their substrates. In general terms, proteins that do not use topological restraint appear to achieve processivity by using a large interaction surface. This allows the enzyme to bind with moderate affinity at a multitude of adjacent sites distributed along its polymeric substrate. At the same time, the use of a large interaction surface minimizes the possibility that the enzyme might bind at a small number of sites with much higher affinity, which would interfere with sliding. Proteins that can both slide along a polymeric substrate, and, as well, recognize highly specific sites (e.g., some site‐specific DNA‐binding proteins) appear to undergo a conformational change between the cognate and noncognate‐binding modes.

Từ khóa


Tài liệu tham khảo

Adam G., 1968, Structural chemistry and molecular biology, 198

10.1074/jbc.272.3.1791

10.1002/pro.5560070701

10.1074/jbc.272.5.2709

10.1093/nar/26.7.1713

10.1016/0968-0004(82)90075-5

10.1038/81978

Brody R.S., 1986, Processivity and kinetics of the reaction of exonuclease I from Escherichia coli with polydeoxyribonucleotides, J. Biol. Chem., 261, 7136, 10.1016/S0021-9258(17)38366-7

10.1021/bi9907429

10.1016/S0021-9258(18)62316-6

10.1073/pnas.90.17.8174

10.1074/jbc.270.23.13850

10.1126/science.288.5466.640

10.1038/34593

10.1016/S0021-9258(19)39784-4

10.1016/0921-8777(93)90019-D

Holtje J.V., 1996, Lytic transglycosylases, EXS, 75, 425

10.1126/science.282.5394.1669

10.1080/10409230091169195

10.1038/nsb0994-638

10.1016/0092-8674(92)90445-I

Kornberg A., 1992, DNA Replication

10.1126/science.277.5333.1824

10.1016/0092-8674(94)90014-0

10.1038/13305

10.1093/emboj/19.6.1228

10.1128/jvi.71.11.8416-8428.1997

10.1126/science.7725097

10.1042/bj3350409

10.1021/bi9530649

10.1006/jmbi.1999.3511

Modrich P., 1975, Bacteriophage T7 deoxyribonucleic acid replication in vitro. A protein of Escherichia coli required for bacteriophage T7 DNA polymerase activity, J. Biol. Chem., 250, 5508, 10.1016/S0021-9258(19)41211-8

10.1038/35000249

10.1016/S0092-8674(00)81483-X

10.1021/bi00415a055

10.1006/jmbi.1999.3477

Nardone G., 1986, Differences in the kinetic properties of BamHI endonuclease and methylase with linear DNA substrates, J. Biol. Chem., 261, 12128, 10.1016/S0021-9258(18)67212-6

10.1038/368660a0

10.1126/science.7624794

10.1093/emboj/17.17.5214

10.1016/S0921-8777(00)00026-4

10.1093/emboj/17.19.5551

10.1021/bi001139p

10.1146/annurev.biochem.69.1.651

10.1006/abbi.1994.1521

10.1038/nsb1097-810

10.1016/S0092-8674(00)80871-5

10.1093/nar/26.10.2374

10.1038/364593a0

10.1021/bi00089a006

10.1093/emboj/19.23.6546

10.1016/S0969-2126(00)00521-9

10.1016/S0021-9258(18)47718-6

10.1016/S0021-9258(17)38226-1

10.1038/367750a0

10.1016/S0969-2126(00)80051-9

Varrot A., 1999, Crystal structure of the catalytic core domain of the family 6 cellobiohydrolase II, Cel6A, from Humicola insolens, at 1.92Å resolution, Biochem. J., 337, 297, 10.1042/bj3370297

10.1021/bi9903998

10.1016/S0092-8674(00)80716-3

10.1016/S1097-2765(00)80329-9

10.1016/S0021-9258(19)84994-3

10.1111/j.1749-6632.1994.tb52803.x

10.1073/pnas.94.24.12754

10.1038/nsb0996-740

10.1016/S0092-8674(00)81515-9

10.1016/S0969-2126(99)80171-3

10.1016/S1097-2765(00)80422-0

Thông tin
Thông tin xuất bản

Protein Science

Tập 10 Số 9

1699-1711

Thông tin tác giả